Running mriqc¶
“Bare-metal” installation (Python 2/3)¶
The software automatically finds the data the input folder if it follows the BIDS standard [BIDS]. A fast and easy way to check that your dataset fulfills the BIDS standard is the BIDS validator.
Since mriqc
follows the [BIDSApps] specification, the execution is
split in two consecutive steps: a first level (or participant
) followed
by a second level (or group
level).
In the participant
level, all individual images to be processed are run
through the pipeline, and the MRIQC measures are extracted and
the individual reports (see The MRIQC Reports) generated.
In the group
level, the IQMs extracted in
first place are combined in a table and the group reports are generated.
The first (participant
) level is executed as follows:
mriqc bids-dataset/ out/ participant
Please note the keyword participant
as fourth positional argument.
It is possible to run mriqc
on specific subjects using
mriqc bids-dataset/ out/ participant --participant_label S001 S002
where S001
and S002
are subject identifiers, corresponding to the folders
sub-S001
and sub-S002
in the BIDS tree.
Here, it is also accepted to use the sub-
prefix
mriqc bids-dataset/ out/ participant --participant_label sub-S001 sub-S002
Note
If the argument --participant_label
is not provided, then all
subjects will be processed and the group level analysis will
automatically be executed without need of running the command in item 3.
After running the participant
level with the --participant_label
argument,
the group
level will not be automatically triggered.
To run the group level analysis:
mriqc bids-dataset/ out/ group
Examples of the generated visual reports are found in mriqc.org.
Depending on the input images, the resulting outputs will vary as described next.
Containerized versions¶
If you have Docker installed, the quickest way to get mriqc
to work
is following the running with docker guide.